Boolean Modifier Dissapearing
For animaton you need to create keyframes, that are inserting by pressing I. Creating or removing smf are not a operation that can be keyframed. 

Instead of this try to animate displaying of modifier. So do the following:


Go to the 1 frame
Hover cursor on eye icon  and/or camera icon and press I
Go to a frame that you want to hide modifier 
Disable modifier (eye icon disables in viewport, camera - in render)
Hover cursor on eye icon  and/or camera icon and press I




It will create an animation, that will hide modifier after chosen frame

For creating a hole, I recommend to create a copy of cylinder, that will not leave a cube, and make them invisible for render:



You can do it in outliner.